chr3-9877092-A-G

Variant names:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001321142.2(CIDEC):c.181T>C(p.Tyr61His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0102 in 1,553,410 control chromosomes in the GnomAD database, including 378 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.018 ( 53 hom., cov: 32)

Exomes 𝑓: 0.0094 ( 325 hom. )

Consequence

CIDEC
NM_001321142.2 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.0900

Variant links:

Genes affected

CIDEC (HGNC:24229): (cell death inducing DFFA like effector c) This gene encodes a member of the cell death-inducing DNA fragmentation factor-like effector family. Members of this family play important roles in apoptosis. The encoded protein promotes lipid droplet formation in adipocytes and may mediate adipocyte apoptosis. This gene is regulated by insulin and its expression is positively correlated with insulin sensitivity. Mutations in this gene may contribute to insulin resistant diabetes. A pseudogene of this gene is located on the short arm of chromosome 3. Alternatively spliced transcript variants that encode different isoforms have been observed for this gene. [provided by RefSeq, Dec 2010]

CIDEC links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.009500384).

BP6

Variant 3-9877092-A-G is Benign according to our data. Variant chr3-9877092-A-G is described in ClinVar as [Benign]. Clinvar id is 128771.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CIDEC	NM_001321142.2 link	c.181T>C	p.Tyr61His	missense_variant	Exon 4 of 7	ENST00000336832.7	NP_001308071.1	Q96AQ7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CIDEC	ENST00000336832.7 link	c.181T>C	p.Tyr61His	missense_variant	Exon 4 of 7	1	NM_001321142.2	ENSP00000338642.2		Q96AQ7-1

Frequencies

GnomAD3 genomes

AF:

0.0175

AC:

2657

AN:

152180

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0354

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.0204

Gnomad ASJ

AF:

0.0109

Gnomad EAS

AF:

0.00731

Gnomad SAS

AF:

0.0810

Gnomad FIN

AF:

0.00697

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00423

Gnomad OTH

AF:

0.0182

GnomAD3 exomes

AF:

0.0184

AC:

2935

AN:

159410

Hom.:

AF XY:

0.0206

AC XY:

1731

AN XY:

83938

show subpopulations

Gnomad AFR exome

AF:

0.0338

Gnomad AMR exome

AF:

0.0171

Gnomad ASJ exome

AF:

0.0107

Gnomad EAS exome

AF:

0.00571

Gnomad SAS exome

AF:

0.0697

Gnomad FIN exome

AF:

0.00645

Gnomad NFE exome

AF:

0.00459

Gnomad OTH exome

AF:

0.0139

GnomAD4 exome

AF:

0.00943

AC:

13211

AN:

1401112

Hom.:

325

Cov.:

AF XY:

0.0110

AC XY:

7627

AN XY:

691208

show subpopulations

Gnomad4 AFR exome

AF:

0.0371

Gnomad4 AMR exome

AF:

0.0163

Gnomad4 ASJ exome

AF:

0.0109

Gnomad4 EAS exome

AF:

0.00249

Gnomad4 SAS exome

AF:

0.0695

Gnomad4 FIN exome

AF:

0.00607

Gnomad4 NFE exome

AF:

0.00398

Gnomad4 OTH exome

AF:

0.0145

GnomAD4 genome

AF:

0.0175

AC:

2667

AN:

152298

Hom.:

Cov.:

AF XY:

0.0189

AC XY:

1410

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.0355

Gnomad4 AMR

AF:

0.0204

Gnomad4 ASJ

AF:

0.0109

Gnomad4 EAS

AF:

0.00733

Gnomad4 SAS

AF:

0.0809

Gnomad4 FIN

AF:

0.00697

Gnomad4 NFE

AF:

0.00423

Gnomad4 OTH

AF:

0.0199

Alfa

AF:

0.00670

Hom.:

Bravo

AF:

0.0169

TwinsUK

AF:

0.00378

AC:

ALSPAC

AF:

0.00441

AC:

ESP6500AA

AF:

0.0314

AC:

136

ESP6500EA

AF:

0.00236

AC:

ExAC

AF:

0.0109

AC:

1137

Asia WGS

AF:

0.0460

AC:

160

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Jun 10, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

not specified

Benign:1

Nov 04, 2013

Genetic Services Laboratory, University of Chicago

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

CIDEC-related disorder

Benign:1

Oct 17, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.056

BayesDel_addAF

Benign

-0.73

BayesDel_noAF

Benign

-0.77

CADD

Benign

1.6

DANN

Benign

0.26

Eigen

Benign

-1.3

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.013

LIST_S2

Benign

0.27

T;T;T;.;T

MetaRNN

Benign

0.0095

T;T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-1.7

.;N;N;N;.

PrimateAI

Benign

0.28

PROVEAN

Benign

0.88

.;.;N;N;N

REVEL

Benign

0.045

Sift

Benign

0.59

.;.;T;T;T

Sift4G

Benign

0.61

T;T;T;T;T

Polyphen

0.0

.;.;B;.;.

Vest4

0.061

MPC

0.016

ClinPred

0.00029

GERP RS

1.3

Varity_R

0.019

gMVP

0.20

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over